TheSeed - User contributions [en]

SEED Viewer Manual/Annotation

2008-12-05T13:32:36Z

TobiasPaczian: /* Compare Regions */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' stands for [[Glossary#Pair_of_Close_Homologs_.28PCH.29|pair of close homologs]].

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected feature may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the feature.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs must have to the selected CDS in order for its region to be displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. In addition to Start, Stop, Strand and Functional Role of the feature, you can see the columns ''FC'', ''SS'', ''Set'' and ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column lead to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T13:28:02Z

TobiasPaczian: /* Compare Regions */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a [[Glossary#Pair_of_Close_Homologs_.28PCH.29|pair of close homologs]].

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T13:25:37Z

TobiasPaczian: /* Compare Regions */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the chromosomal neighborhood of the feature in its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. Feature overlaps are resolved by drawing the overlapping feature in a new line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. If you are logged in, the numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen feature and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T13:20:53Z

TobiasPaczian: /* Reasons for Current Assignment */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

For information about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. In addition to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T13:19:45Z

TobiasPaczian: /* The Annotation Overview */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row lead to different pages containing other views and information about the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs of papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T13:17:08Z

TobiasPaczian: /* The Annotation Overview */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. To the right of the taxonomy id of the genome you will find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Annotation

2008-12-05T11:31:25Z

TobiasPaczian: /* The Annotation Overview */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by our annotators, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of Similarities and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/Menu

2008-12-05T10:25:48Z

TobiasPaczian: /* FIGfams Menu */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps.

Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to change this selection.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page for [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Menu

2008-12-05T10:24:45Z

TobiasPaczian: /* Feature Menu */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps.

Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to change this selection.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Menu

2008-12-05T10:23:05Z

TobiasPaczian: /* Comparative Tools */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps.

Blasting against your organism is possible using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Menu

2008-12-05T10:22:36Z

TobiasPaczian: /* Comparative Tools */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism onto KEGG maps.

Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Menu

2008-12-05T10:21:38Z

TobiasPaczian: /* Comparative Tools */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphic comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps.

Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Menu

2008-12-05T10:01:10Z

TobiasPaczian: /* Menu Overview */

== Menu Overview ==

The menu is a small bar below the logo of each page. Most menus have submenus that can be accessed via hovering over the menu. Click the submenu entry you want to go to. If no submenu is present, you can directly click the menu itself.

=== Navigate Menu ===

This menu is present on every SeedViewer page. The first entry '''Startpage''' will lead to the SeedViewer [[SEED_Viewer_Manual|HomePage]].

'''Organisms''' will open the [[SEED_Viewer_Manual/OrganismSelect|Organism Select]] page. You will see an overview of all organisms in the SEED and are able to select one to view in detail.

'''Subsystems''' will do the same for subsystems.

'''Scenarios''' lets you browse [[Glossary#Scenarios|Scenarios]] on the [[SEED_Viewer_Manual/Scenarios|Scenarios Page]].

'''FIGFams''' leads to an entry point for browsing [[SEED_Viewer_Manual/FIGfams|FIGfams]]. You can find more information about FIGfams [[Glossary#FIGfam|here]].

The '''BLAST Search''' links to the [[SEED_Viewer_Manual/BLASTOrganism|BLAST Page]]. You will be able to BLAST a sequence against an organism in the SEED.

[[Image:MenuNav.png]]

=== Help Menu ===

This menu is also present on all SeedViewer pages. The first link '''What is the SEED''' will lead you to the [[Home_of_the_SEED|SEED Homepage]].

Clicking the second link '''How to use the SEED Viewer''' will get you to this wiki.

'''Submitting data to SEED''' lets you browse the [[RAST_Tutorial|RAST Tutorial]].

'''Contact''' enables you to write an email to the SEED team.

Clicking '''Register''' is the first step to get a user account. It will lead to the [[SEED_Viewer_Manual/Register|Register]] page.

'''I forgot my password''' enables you to [[SEED_Viewer_Manual/RequestNewPassword|Request a new password]].

[[Image:MenuHelp.png]]

=== Organism Menu ===

In the context of a selected organism, an organism menu will appear. '''General Information''' will lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] of the selected organism.

The '''Feature Table''' will open the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and show you the features present in that organism.

'''Genome Browser''' leads to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.

Clicking '''Scenarios''' shows the [[SEED_Viewer_Manual/Scenarios|Scenarios]] page for your organism.

'''Subsystems''' opens a page that lets you select subsystems.

'''Export''' enables you to [[SEED_Viewer_Manual/DownloadOrganism|download]] the features of your organism.

[[Image:MenuOrganism.png]]

=== Comparative Tools ===

This menu is also present whenever an organism is viewed. Different kinds of comparisons of your selected organism to other organisms are available here.

'''Function based Comparison''' - The [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one.

The '''Sequence based Comparison''' [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based).

Use the '''KEGG Metabolic Analysis''' [[SEED_Viewer_Manual/KEGG|to project the metabolic capabilities]] of your organism on KEGG maps.

Blasting against your organism is enabled using the '''[[SEED_Viewer_Manual/BLASTOrganism|BLAST Search]]'''.

[[Image:CompTools.png]]

=== Feature Menu ===

Whenever a feature is defined on a SeedViewer page, you will find the '''Feature''' menu for that feature.

The '''Feature Overview''' points to the [[SEED_Viewer_Manual/Annotation|Annotation]] page. It shows general information about the feature, als well as a Compare Regions View that displays the feature in its genomic context and in comparison to homologs in other genomes.

'''DNA Sequence''' will open a page with the DNA Sequence of the feature (in FASTA format). '''DNA w/ flanking''' not only prints the DNA sequence of the feature, but also includes a user-defined number of bases upstream and downstream of the feature. '''Protein Sequence''' will show you the protein FASTA sequence (translated from the DNA sequence) of the feature.

'''Feature Evidence vs. FIG''' and '''Feature Evidence vs. all DB''' link to the [[SEED_Viewer_Manual/Evidence|Evidence]] page. The difference between the two is that the evidence shown for the feature includes only evidence against features in the SEED or also against other databases (e.g. GenBank, SwissProt, UniProt and many others). The evidence page will also allow you to make this selection or change it there.

[[Image:MenuFeature.png]]

=== Feature Tools ===

This menu is also present if a feature is defined. It lets the user run a variaty of tools using the feature sequence. These include tools that look for transmembrane helices (e.g. [http://www.cbs.dtu.dk/services/TMHMM/ TMHMM]), signal peptides ([http://www.psort.org/ PSORT], [http://www.cbs.dtu.dk/services/SignalP/ SignalP]), protein domains (e.g. [http://www.ebi.ac.uk/interpro/ InterPro], [http://prodom.prabi.fr/prodom/current/html/home.php ProDom]) and others.

[[Image:MenuFeatTools.png]]

=== FIGfams Menu ===

On SeedViewer pages that deal with [[Glossary#FIGfam|FIGfams]], you will find an additional FIGfams menu. The '''Home''' link leads to the entry page to [[SEED_Viewer_Manual/FIGfams|FIGfams]].

The '''Release History''' will lead you to a [[SEED_Viewer_Manual/FIGfamsRelease|page]] containing a number of statistics about the current release of the FIGfams.

'''Download''' will connect you to the FTP server to enable you to download the FIGfams.

[[Image:MenuFIGfam.png]]

SEED Viewer Manual/Annotation

2008-12-03T20:02:36Z

TobiasPaczian: /* Compare Regions */

== Annotation ==

The Annotation page shows a variaty of information about a single feature like a protein or an RNA. The page is roughly divided into three parts. The '''Annotation Overview''' presents the basic information about the feature. '''Reasons for Current Assignment''' reflect why the feature was assigned with the current functional role. The third part is a '''Compare Regions View''' showing the region of the feature in context to its own and related genomes.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Annotation|here]].

=== The Annotation Overview ===

The feature ID and the genome it belongs to are shown in the header line of this part of the page. They link to [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] and the [[SEED_Viewer_Manual/OrganismPage|Organism Page]], respectively.

The '''current annotation''' depicts the functional role that is currently assigned to the feature. As annotations can be changed by users, you have the option to view an annotation history by pressing the '''show''' button in the cell '''annotation history''' some rows below. It will open a small table listing the date, the curator and the annotation that was made for each entry.

As the genome name for the feature is already presented in the header of this section, we additionally show the '''taxonomy id''' for that genome in the overview. The link will lead to the Taxonomy Browser at the NCBI showing the taxonomy information for that genome. Behind the taxonomy for the genome you can find the '''contig''' the feature can be found on.

The '''internal links''' you can see in the next row are leading to different pages containing other views and information for the feature.
The [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] ('''genome browser''') displays the feature in the context of its genome.
'''evidence''' leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains. Downloading the actual sequence for the feature is possible using the [[SEED_Viewer_Manual/ShowSeqs|Sequence Page]] ('''sequence''') link.

Behind the external links you find a link to the '''ACH''' essentially identical genes. This link leads to the [[AnnotationClearingHouse|Annotation Clearing House]], a collection of proteins from many different sources. Proteins that have essentially the same sequence are grouped. For a given ID, you can see all IDs from different sources that belong to this group.

At '''PubMed Links''' you can see the PubMed IDs to papers linked to the NCBI Entrez Database. The PubMed IDs shown are direct literature links attached directly to a feature, so-called '''dlits'''.

'''FIGfams''' are protein families based on the subsystems technology. If you find an entry in this fields, the feature is part of the stated FIGfam. The link leads to the [[SEED_Viewer_Manual/FIGfams|FIGfam Viewer]].

'''database cross references''' link the feature to its entries (Aliases) in other databases like UniProt, GenBANK and many others.

To gain more information about a feature, you can run different tools (e.g. PSI-BLAST, InterPro and many others) on your feature. Select a tool and press the button '''run tool'''.

[[Image:AnnotationFeat.png]]

=== Reasons for Current Assignment ===

To gain a clue about what evidence an assignment of a functional role to your feature is based on, the text in '''Reasons for Current Assignment''' summarizes important information supporting the annotation. Additional to the information in the overview table, a list of indirect literature ('''ilits''') is decribed in the text. Those are based on direct literature to similar features that have the same functional role.

[[Image:AnnotationAnnot.png]]

=== Compare Regions ===

The first line of the '''Compare Regions''' is a graphical display of the region of the feature its genome. All proteins are shown as colored arrows, where the direction depicts the strand of the feature. RNAs and other features are small boxes on the line. If two features overlap, the overlapping will be drawn on an (invisible) second line.

The graph is centered on the selected feature (numbered 1), which is always colored red. Below you find the same region for orthologs in other (related) organisms, also colored in red. The colors of the other features (as well as the numbers) also represent ortholog (or sometimes also paralog) features. Whenever there are at least two ortholog or paralog features of a kind, a color (and a number) is assigned to them.

'''Display Options''' are divided into two ''Regular'' and ''Advanced''.

In the '''Regular''' options, you can change the ''Region Size'' and the ''Number of Regions''. Changing the '''Region Size''' enables to zoom in or out of the region. Changing the '''Number of Regions''' will add or remove genomes to your display. Click '''update graphics''' to change the display. The numbers that you put in for these values will be saved as [[SEED_Viewer_Manual/Preferences|preferences]].

[[Image:AnnotationComp.png]]

If you click '''Advanced''' options, you will see the default options that are used for the Compare Regions View.
The '''Pinned CDS Selection''' refers to the chosen peg and its orthologs in other genomes. The selection of genomes to show in the graphics can be made by ''Similarity'' or ''PCH pin''. The default is '''Similarity''' and means that the genomes are chosen using the similarity of the selected genes to its orthologs in other genomes.
A '''PCH''' means a ''pair of close homologs''. [...]

In the cell '''Genome Selection''' you can choose to ''collapse close genomes''. For many organism groups, the SEED database contains a number of strains that do not differ too strongly. They can be removed from the display using this option.

The genomes in the display can be sorted by '''Phylogeny''' or '''Phylogenetic distance to input CDS'''. In the first case, the genome of the selected peg may not appear on the first line any more, but the genomes in the display are sorted by the overall phylogeny. The second (default) options will show the selected CDSs region on the first line and the other genomes in order of phylogenetic distance to the peg.

The '''Evalue cutoff for selection of pinned CDSs''' depicts the minimum similarity CDSs may have to the selected CDS so that the its region is displayed.

Defining if CDSs are orthologs or paralogs to a given CDS and therefore colored as such can be done using the '''Evalue cutoff for coloring CDS sets'''.

We have implemented two different '''Coloring algorithms''' for the display. Default is a fast algorithm that might not always be absolutely accurate. You can choose a slower, but exact algorithm for coloring if you are unsure.

[[Image:AnnotationAdv.png]]

The second tab of the Compare Regions tab view lists all visible features in a table, sorted by the genome they appear in. The entries in the '''ID''' column link to the Annotation page of the feature. Additional to Start, Stop, Strand and Functional Role of the feature, you can see a column ''FC'', an ''SS'', a ''Set'' and a ''CL''. '''FC''' stands for ''[[Glossary#Functional Coupling|Functionally coupled]]'', showing the number of features that are coupled to this feature via clustering genomes or other evidence. The '''SS''' column shows the subsystems the feature is in. '''Set''' is the number that is depicted above a colored feature in the graphic. The '''cluster''' buttons in the last column leads to the [[SEED_Viewer_Manual/HomologClusters|Homolog clusters]] page for that feature.

[[Image:AnnotationTabl.png]]

SEED Viewer Manual/FunctionalRoles

2008-12-03T19:30:43Z

TobiasPaczian: /* Functional Role Page */

== Functional Role Page ==

This page displays a functional role in context of a subsystem. The left part of the top table shows the '''Functional Role''' and the context '''Subsystem'''. If present, an '''EC-number''' or '''GO-number''' and '''Reactions''' are listed. The EC-number links to the [http://www.genome.ad.jp/kegg/ KEGG] enzyme page for the enzyme. GO-numbers are [http://www.geneontology.org GeneOntology] classifications for a role. The link leads to the GO-Viewer [http://amigo.geneontology.org/cgi-bin/amigo/search.cgi AmiGo]. Reactions are [http://www.genome.ad.jp/kegg/ KEGG] reactions that are bound to the EC-number.

The right part of the table gives an overview of the assignments of the functional role to SEED features. '''Number of Occurrences''' is the total number of features that are assigned with the role. '''Number of Organisms''' is the number of different organisms that contain at least one feature assigned with the role. Then they are devided by domains of the organisms (Archaea, Bacteria, Eukaryota or Virus).

[[Image:FunctionalRole1.png]]

The table below lists all features that are assigned with the functional role. The feature ID links to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for the feature. The organism link in the second column of the table points to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]] for that organism. The domain of the organism is depicted in the third column.

You can download the table in ''comma-separated format'' using the '''export table''' button. To gain access the sequences of the listed features, press the '''show sequences''' button that opens the [[SEED_Viewer_Manual/ShowSeqs|Sequence]] page.

[[Image:FunctionalRole2.png]]

SEED Viewer Manual/Subsystems

2008-12-03T19:23:45Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table above the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T19:22:44Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table). Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T19:21:35Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant of this subsystem, it is not implement this organism.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T18:20:23Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), enter '''yes''' into the filter in the column header. For seeing only the not active ones, enter '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T18:19:53Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or inactive variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T18:17:45Z

TobiasPaczian: /* Spreadsheet */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T18:16:04Z

TobiasPaczian: /* Functional Roles */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. It is used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Subsystems

2008-12-03T18:09:49Z

TobiasPaczian: /* Subsystems */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can for example be a metabolic pathway or a component of a cell like a secretion system.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

WebComponents/Table

2008-11-26T17:00:09Z

TobiasPaczian: /* Export */

== Table ==

The Table component has a large number of functionalities that can be used to access data that can be displayed in tabular form. Features of the table component are '''Browsing''', '''Sorting''', '''Filtering''' and '''Export'''. Most of these functions of the table are implemented by JavaScript functions. That means, it does not lead to a reload of the page. The page ''knows'' all the information, but only part of it is displayed. The display is then manipulated using JavaScript functions.

A table consists of a header row (here in dark blue) and the rows that contain the data. In some cases the header row can be supplied with a supercolumn to group columns. The header cells contain the functionality to sort and filter the row data, as described below.

The rows are colored in two different colors for better visibility (here white and light grey background). If you hover over a row, it will be highlighted in dark grey.

[[Image:Table1.png]]

=== Browsing ===

The number of rows you want your table to display at once can be changed using the text box '''display ___ items per page'''. Just press return after changing the number to change the display of your table.

To browse through the table you can click the links '''<<first''', '''<<prev''', '''next>>''' and '''last>>'''. The links only appear if there is e.g. a next page. The text in the middle of the links will tell you which items are currently displayed.

[[Image:TableBrowse.png]]

=== Sorting ===

You can sort the contents of the table by each column using the little arrows next to the column header. The sorting is done using JavaScript, meaning that it does not reload the page.

[[Image:TableSort.png]]

=== Filtering ===

Different kinds of filters can be applied to the table data. The table always uses all filters for all columns at once. This means that if you may want to check if other filters are active, if the result of filtering a column is not what you expect. Often, a '''clear all filters''' button is made available on top of the page.

One filter is simply a text field that does an infix search (meaning that if the word you type in the text field is part of a word in the cells of a cell in the respective column, the row will be visible).

[[Image:TableFilter1.png]]

The combo box filter is usually used if only a small number of different values are used in a column. These values appear in the combo box if you click the arrow next to the textfield. Choose one and the table will filter automatically.

[[Image:TableFilter2.png]]

If a column consists of numbers, you will often get a filter using operators ('''>''', '''<''', '''=''' and others). You can choose one of these operators, and put a number into the text field below the operator to filter the table.

[[Image:TableFilter3.png]]

=== Export ===

For most tables, you will find an '''export''' button on the page. This will let you download the data of the table in '''.tsv''' format. This tab-separated text can be opened with many editors and spreadsheet tools (i.e. Microsoft Excel).

SEED Viewer Manual/Subsystems

2008-11-26T16:55:35Z

TobiasPaczian: /* Subsystems */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component of a cell like a secretion system and others.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponents/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

WebComponents/Tabview

2008-11-26T11:42:53Z

TobiasPaczian: /* The TabView */

== The TabView ==

The TabView component is used on many pages in the [[SEED_Viewer_Manual|SeedViewer]]. It is useful at places where you have different options to access data or you need to fulfill a task step-by-step.

The entire content of the TabView is loaded when you enter the page. Clicking a different tab only displays the data which was hidden before.
At the top of the TabView, you can access the different tabs. In the example (SeedViewer Mainpage), the chosen tab is white, while all hidden tabs have a green header. Click on the green header to activate the respective tab.

[[Image:TabView.png]]

SEED Viewer Manual/Subsystems

2008-11-25T16:56:22Z

TobiasPaczian: /* Subsystems */

== Subsystems ==

A [[Glossary#Subsystem|subsystem]] is a collection of [[Glossary#Functional role|functional roles]] that are associated to each other in a system. Such a system can be a metabolic pathway, a component of a cell like a secretion system and others.

The subsystem page in the SeedViewer is divided into different parts via a [[WebComponent/Tabview|TabView]]. The TabView can consist of 3-5 tabs. The first tab shows a '''Diagram''' of the subsystem, the second tab displays a [[WebComponents/Table|table]] with the '''Functional Roles''' present in the subsystem. The '''Spreadsheet''' showing relating the functional roles in the subsystem to features in genomes can be found in the third tab. The fourth and fifth tab show a description and additional notes to a subsystem. They only appear if a subsystem has a description / notes.

=== Diagram ===

The subsystem diagram shows the connections between the functional roles in a subsystem. The boxes represent the functional roles via their abbreviations. The circles are connecting intermediates, that are described in the table which is part of the diagram.

The functional roles in the diagram can be colored according to their presence in a genome. Click the button '''Color Diagram''' to get a combo box with all genomes in the subsystem. Select your genome of interest and press '''do coloring'''. The boxes for the functional roles defined for that genome will now be colored in green.

[[Image:SubsystemDiagram.png]]

=== Functional Roles ===

This [[WebComponents/Table|table]] lists all functional roles present in the subsystem. The first column shows '''Group Aliases''' for the functional role. Functional roles can be aggregated in groups (subsets). Subset names that start with a '*' contain alternative ways to implement a function.

The abbreviation ('''Abbrev.''') for a functional role must be unique for the functional roles in the subsystem. They are used in different displays like the Diagram or the Speadsheet.

The third column lists the full name of the functional role. EC-Numbers are often part of the functional role (for enzymes), and are stated in parentheses after the name of the functional role.

The following two columns deal with reactions a functional role is connected to. Clicking on the link opens a new window showing the KEGG reaction. Next to annotator-curated KEGG reactions, we show the KEGG reactions of the curation effort of the [[SEED_People#Hope College|Hope College]] team that collaborates with the SEED.

GeneOntology (GO) links are displayed in the next column. The links point to the GO-number in GeneOntology's Amigo-Tool.

The last column can contain literature (PubMed IDs) that describes the functional role in detail. If present, you will find a link to PubMed in this column.

[[Image:SubsystemFRs.png]]

=== Spreadsheet ===

The subsystem spreadsheet displays the features that are assigned with the functional roles in all organisms that are part of the subsystem.

The organisms are displayed in the first column. The links lead to the [[SEED_Viewer_Manual/OrganismPage|Organism Page]]. The column header includes a filter option for the organism, doing an infix search on the organism name.

The '''Domain''' (Bacterial, Archaeal or Eukaryote) of the organism is shown in the second column.

For each organism in the spreadsheet, a '''Variant Code''' is assigned. Usually, there is more than one way to fulfill a subsystem. Metabolic pathways can have alternatives, or parts of the pathway may be present or absent in an organism. [[[Glossary/Variant Code|Variant Codes]] are assigned to the organism to express this behavior. There are two special Variant Codes: '''0''' and '''-1'''.

The Variant Code '''-1''' means that the organism has no active variant in this subsystem, meaning it does not implement the subsystem.

'''0''' means that the curator has not yet assigned a variant to the genome. Due to the flow of newly sequenced genomes into the SEED, this variant code may show up sometimes.

The next column is used to filter active or not active variants. If you want to see only the active ones (default), print '''yes''' into the filter in the column header. For seeing only the not active ones, print '''no'''. No input in this field will show all variants.

All following columns in the table show the features in the organisms that are assigned with functional roles. The column headers display the abbreviations of the functional roles (see Functional Roles Table) Hovering over a column header will show a tooltip with the full name of the role. The feature entries in the cells for the functional roles are linked to the [[SEED_Viewer_Manual/Annotation|Annotation Page]] for that feature. There can be multiple features in a cell, as some functions are implemented by more that one feature in an organism.

The control table on top of the spreadsheet table lets you change the display in the table:

Functional Roles that belong to a subset starting with a '*', meaning they are alternatives for a function, are collapsed in the spreadsheet by default. If you want to expand the subsets, you can do so by checking '''expanded''' in the '''Subsets''' column.

The feature entries in the spreadsheet can be colored according to different metaphors using the second column ('''Coloring''') of the table. By default, the features are colored '''by cluster'''. In this case, it is computed which features are close by on the genomic sequence, meaning they cluster. Each computed cluster gets its own color. These colors only have a meaning per genome, meaning that a yellow cluster in one genome has no connection to a yellow cluster in the next genome. Another way to cluster the features are different kinds of attributes. Check the radio box for '''by attribute''' and choose an attribute in the drop down menu. Press '''update''' to change the display.

[[Image:SubsystemSpreadsheet.png]]

=== Description ===

The description of a subsystem gives an overview of the functional roles and their connections in the subsystem. It can give some background information about the system, what organisms it is usually found in and other facts that are of interest.

=== Additional Notes ===

As the description already gives an overview over the subsystem, additional notes can be found here. The notes usually refer to specific properties of some organisms or organism groups, genes that are missing but should be there and other details that might be useful for the interested user.

SEED Viewer Manual/Evidence

2008-11-25T14:08:11Z

TobiasPaczian: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED and other databases, as described at [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Evidence

2008-11-25T13:59:49Z

TobiasPaczian: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two functions via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Evidence

2008-11-25T13:58:44Z

TobiasPaczian: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. To the right of the checkbox you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Evidence

2008-11-25T13:57:21Z

TobiasPaczian: /* Similarities */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED and other databases. The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/Evidence

2008-11-25T13:56:40Z

TobiasPaczian: /* Domains */

The Evidence Page is divided into two parts via a [[WebComponents/Tabview|TabView]]: The '''Visual Protein Evidence''' and the '''Tabular Protein Evidence'''.

If you are logged in and the feature belongs to your private genome, this page will have additional options for you to annotate the feature. These are described [[SEED_Viewer_Manual/Editing_Capabilities/Evidence|here]].

== Visual Protein Evidence ==

After loading the Evidence Page, the first tab of the [[WebComponent/Tabview|TabView]] is selected. It visually shows different pre-computed tool results for the given feature. In this view, you can see evidence for ''Location'' of the product of the gene in the cell, evidence for protein ''Domains'' and evidence that show ''Similarities'' to other features.

=== Location ===

'''Location''' stand for location of the product of the feature in the cell. This section presents output for tools that look for transmembrane helices (TM) or signal peptides (SP) in the feature. In the example, you can see five transmembrane helices in the protein identified via the Phobius tool. They are visualized as little boxes, and their location on the line depicts the location of the transmembrane helices in the protein.

[[Image:EvidenceLocation.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the full length of the protein).

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomain.png]]

=== Similarities ===

This section graphically lists evidence for similarities to other features in the SEED database (or also other databases). The '''E-Value Key''' shown on the top defines the colors that are used to display different E-Value ranges for the similarities to the hit features. Hovering over the E-Value Key shows the value range for each color.

Each similarity is represented by two bars, showing the alignment of the similarity. The first bar is the '''query''' feature, the second the '''hit''' feature. The abbreviation in front of this bar informs you about the organism the hit feature is in. Hover over the abbreviation to get the complete organism name. Behind the box you can find the [[Glossary#Functional role|functional role]] of the hit feature.

The length of the outside box shows the complete length of the respective sequence. The color of the outside box represents the range of the evalue score according to the E-Value Key bar. The length of the inner (white) box depicts the actual section of the sequence the similarity to the other feature is in. Hovering over the box will show you some information about the hit feature (see tooltip graphics below), including the [[Glossary#Functional role|functional role]], the [[Glossary#Subsystem|subsystems]] and some values describing the hit area.

If you check some of the checkboxes in front of the [[Glossary#Functional role|functional role]] descriptions of the hit genes, you can access two function via the buttons on top of the Similarity graphics. The button '''Align Selected''' leads to an [[SEED_Viewer_Manual/AlignSeqs|alignment page]] showing a TCoffee alignment for the selected features. '''FASTA Download Selected''' lets you download the selected sequences in aminoacid FASTA format.

[[Image:EvidenceSims1.png]]

[[Image:EvidenceHoverSim.png]]

To change the evidence view with respect to the sorting and the filtering of the hits, you can find a little control box on top of the similarity graphics. '''Max Sims''' is the number of similarities that are listed on the page. '''Max E-Value''' filters out all similarities that have a higher E-Value than stated here. In the little combo box below these two values, you can decide to see only hits against the SEED database ('''Just FIG IDs'''), or also against other databases ('''Show all Databases'''). You can '''Sort''' the '''Results By''' ''Score'', ''Percent Identity'' (default) or ''Score per position''. These values locally refer to the hit as known from BLAST hits, so a high percent identity referring to a very small hit region can make this similarity show up as one of the first hits, as shown in the example. Checking '''Group by Genome''' will aggregate all hits to features in the same genome. A blue box will mark hits that belong to the same genome. After selecting the right values, you can press the button '''Resubmit''' to change the evidence view.

[[Image:EvidenceFil1.png]]

== Tabular Protein Evidence ==

Activate the second tab of the large page-spanning [[WebComponents/Tabview|TabView]] to see the tabular view of the evidence. You will find most of the information already shown in the visual view, presented differently and enriched with some additional information. Added are the '''Identical Proteins''' and the '''Functionally coupled''' sections, while '''Location''' information is not presented in this tab.

=== Similarities ===

The similarity [[WebComponents/Table|table]] lists hits to similar features in the SEED database (or also other databases), like described for the [[SEED_Viewer_Manual/Visual Protein Evidence|Visual Protein Evidence]]. Each row in the table represents a hit.

The first column provides a checkbox to select a hit feature. Again, the buttons '''Align Selected''' and '''FASTA Download Selected''' are present and can be used to get to a TCoffee [[SEED_Viewer_Manual/AlignSeqs|alignment page]] or download the protein sequences of the selected features in FASTA format. The two buttons in the column header allow mass selection of the features. '''All''' will select all features visible in the table, '''check to last checked''' lets you select all features up to a selected feature in the [[WebComponents/Table|table]].

The ID of the hit features, as well as a link to the [[SEED_Viewer_Manual/Annotation|annotation page]] is displayed in the column '''Similar FIG Sequence'''.

The next four columns describe information to the hit regions of the query and hit features ('''E-value''', '''Percent Identity''', '''Region in Query peg''' and '''Region in Similar Sequence''').

The '''Organism''' of the hit peg and its '''Function''' are shown in the next two columns. If the function is different from the function of the query feature, it is colored. Same function in the table will get the same color.

'''Associated Subsystems'' of the feature are displayed in the next column. If the feature is not associated to a subsystem, you will find the text ''None added'' in the cell.

There are three '''Evidence Codes''' that can be found in the last column. ''ISU'' means that the feature is unique in a cell of a subsystem. This means that there is no other feature in the genome that is thought to have the same function. ICW(number) means the feature is clustered with ''number'' features in the genome. ''FF'' says that it is in a [[Glossary#FIGfam|FIGfam]].

The [[WebComponents/Table|table]] can be exported via the button '''export table''' that can be found on top of the table.

[[Image:EvidenceSims2.png]]

You can filter and sort the table using the [[WebComponents/Tabview|TabView]] above the table. The second tab, '''Sims Filter''' works the same way as described for the Similarities in the [[SEED_Viewer_Manual/Evidence#Visual Protein Evidence|Visual Protein Evidence]]. The first tab '''Edit Columns''' contains a number of columns with additional information that can be added to the display of the table ([[Glossary#FIGfams|FIGfams]], different aliases to other databases and many others). Just choose a column name, press the arrow to put it into the right field and it will add it to the table.

[[Image:EvidenceFilter.png]]

=== Domains ===

This section shows pre-computed domains for the selected feature. In the example, you can find a CDD domain and a Pfam domain for the feature. The blue bar marks the location of the domain found in the protein (the line depicts the whole length of the protein).

The [[WebComponents/Table|table]] lists the '''Domain DB''' (the database for the domain that was hit), the '''ID''' in the domain database, the '''Name''' of the domain, the '''Location''' of the hit in the selected feature, the '''Score''' for the hit against the domain, as well as the '''Function''' of the domain.

The table can be exported using the '''export table''' button.

Additional tools can be accessed via the '''[[SEED_Viewer_Manual/Menu#Feature Tools|Feature Tools Menu]]''' in the menu bar.

[[Image:EvidenceDomTable.png]]

=== Identical Proteins ===

'''Essentially Identical Proteins''' are proteins that share a common sequence, but the start position of the proteins may vary a little. This definition was made because in different databases or close strains of organisms, it often happens that a protein is present, but the start position may be shifted in the finding genes step. So essentially, this table shows aliases of the feature that were based on protein identity.

The first column of the [[WebComponents/Table|table]] shows the '''Database''' the alias can be found in, while the second column ('''ID''') offers the alias name and a link to the protein in the respective database. The following two columns describe the '''Organism''' and the '''Assignment''' for the feature for the alias.

[[Image:EvidenceEIPs.png]]

=== Functionally Coupled ===

This [[WebComponent/Table|table]] lists all [[Glossary#Functional coupling|functionally coupled]] genes in the organism. You can see the '''Score''', the '''ID''' of the feature and the '''Function''' of the feature.

[[Image:EvidenceFCs.png]]

SEED Viewer Manual/GenomeBrowser

2008-11-21T11:01:04Z

TobiasPaczian: /* The Six Frame View */

== Genome Browser ==

The Genome Browser enables you to view the features of a genome in their genomic context. The page is divided into three parts, a Control [[WebComponents/Tabview|TabView]], the Six Frame View, and a [[WebComponents/Table|table]] showing all features of an organism.

=== The Six Frame View ===

The six frame view represents the six reading frames for proteins (-3, -2, -1, 1, 2, 3). Blue arrows are printed representing protein features. Their direction depicts the strand of the protein (- or +).

As RNA features (tRNAs, rRNAs, or other genomic features like binding sites) have no reading frames. They can be found in the middle line of the image, represented by little blue boxes.

Hovering over a feature will show a tooltip containing information about the feature, including the name, the position in the genome, the [[Glossary#Functional_role|functional role]] and the [[Glossary#Subsystem|subsystem(s)]] it's in.

[[Image:GenomeBrowser6fw.png]]

=== The Control TabView ===

Controlling the Six Frame View can be done using the first tab ('''Location''') of the Control TabView. You can choose a location the of the genome you want to view by selecting a contig in the '''contig''' drop down menu and stating a '''start position''' on that contig. The zoom of the window can be changed using the '''window''' drop down box.

In addition, features can be colored by different metaphors: by subsystem, by filter options of the Feature Table (the features that are present in the table after filtering it will be colored) or by a user defined list you can specify in the '''Upload List''' tab.

Click the button '''Draw''' after making your selections. The arrows '''<=''' and '''=>''' will shift the window over the contig sequence.

If you have selected a feature in the Six Frame View, the second tab ('''Focus''') will show you information about the feature (the same information you can find in the tooltip by hovering over the feature). Additionally, you will get three buttons that lead to pages that show more detailed information about the selected feature.

The button '''zoom to sequence''' will show you the '''[[SEED_Viewer_Manual/ContigView|DNA to Protein]]''' page depicting a detailed sequence view including the DNA sequence, a six frame view of the translation to protein and other features of the sequence in the area of the selected feature.

Clicking '''details page''' leads to the [[SEED_Viewer_Manual/Annotation|Annotation]] page of the feature. You will see all known details about the feature, as well as the [[SEED_Viewer_Manual/Annotation#CompareRegions|Compare regions view]] centered on the feature.

The '''evidence''' button leads to the [[SEED_Viewer_Manual/Evidence|Evidence]] page showing evidence for the annotation of the feature in form of [[Glossary/Similarities|Similarities]] and protein domains.

'''Upload a list''' - will let you upload a list of locations of BLAST hits of the form (Contig, Start, Stop, ID). The list has to be in plain text format, meaning not an Excel table. If you have an Excel table containing the information, save the list as '''text (tab delimited)''' in Excel. If you have successfully uploaded a list, you will now be able to navigate the regions in your list. They are shown on the middle line in the Six Frame View in form of little boxes.

[[Image:GenomeBrowserLoc.png]]

=== The Feature Table ===

The Feature Table shows all features present in your organism in a [[WebComponents/Table|table]]. Information you can see for a feature are its ID, Type (e.g. CDS, RNA and others), its locations (Contig, Start, Stop) and length as well as the functional role it's annotated with and the subsystems it belongs to. The button in the last column (Region) will center the Six Frame View on this feature and select it.

[[Image:GenomeBrowserFeat.png]]

SEED Viewer Manual/OrganismPage

2008-11-18T14:48:46Z

TobiasPaczian: /* Browse, Compare and Download */

== Organism Page ==

=== Menu and General Information ===

Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].

The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there is an existing Wikipedia page).

If you click on '''click for full list''', you will find more specific information about the organism.

[[Image:OrgsMenuGeneral.png]]

=== Browse, Compare and Download ===

The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu.

'''Browse'''

Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.
It lets you browse the features of your organism.

[[Image:OrgsBrowse.png]]

'''Compare'''

Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link.

[[Image:OrgsCompare.png]]

'''Download'''

This tab provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.

[[Image:OrgsDownload.png]]

=== Subsystem Information ===

This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]].

'''(1) Subsystem Statistics'''

The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems.

In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.

Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism.

[[Image:OrgsSubsystems.png]]

'''(2) Features in Subsystems'''

Click on the second tab of the tab view to get the tabular view of the Features in Subsystems.
The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism.

The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature.

[[Image:OrgsFeatures.png]]

SEED Viewer Manual/OrganismPage

2008-11-18T14:39:02Z

TobiasPaczian: /* Menu and General Information */

== Organism Page ==

=== Menu and General Information ===

Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].

The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there is an existing Wikipedia page).

If you click on '''click for full list''', you will find more specific information about the organism.

[[Image:OrgsMenuGeneral.png]]

=== Browse, Compare and Download ===

The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu.

'''Browse'''

Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.
It lets you browse the features of your organism.

[[Image:OrgsBrowse.png]]

'''Compare'''

Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link.

[[Image:OrgsCompare.png]]

'''Download'''

This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.

[[Image:OrgsDownload.png]]

=== Subsystem Information ===

This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]].

'''(1) Subsystem Statistics'''

The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems.

In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.

Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism.

[[Image:OrgsSubsystems.png]]

'''(2) Features in Subsystems'''

Click on the second tab of the tab view to get the tabular view of the Features in Subsystems.
The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism.

The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature.

[[Image:OrgsFeatures.png]]

SEED Viewer Manual/OrganismPage

2008-11-18T14:38:02Z

TobiasPaczian: /* Menu and General Information */

== Organism Page ==

=== Menu and General Information ===

Two categories are added to the menu bar when visiting an organism page. These are organism specific menus described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].

The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page).

If you click on '''click for full list''', you will find more specific information about the organism.

[[Image:OrgsMenuGeneral.png]]

=== Browse, Compare and Download ===

The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu.

'''Browse'''

Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.
It lets you browse the features of your organism.

[[Image:OrgsBrowse.png]]

'''Compare'''

Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link.

[[Image:OrgsCompare.png]]

'''Download'''

This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.

[[Image:OrgsDownload.png]]

=== Subsystem Information ===

This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]].

'''(1) Subsystem Statistics'''

The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems.

In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.

Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism.

[[Image:OrgsSubsystems.png]]

'''(2) Features in Subsystems'''

Click on the second tab of the tab view to get the tabular view of the Features in Subsystems.
The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism.

The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature.

[[Image:OrgsFeatures.png]]

SEED Viewer Manual/OrganismPage

2008-11-18T14:35:25Z

TobiasPaczian: /* Menu and General Information */

== Organism Page ==

=== Menu and General Information ===

Two categories are added to the menu bar when visiting an organism page. These are organism specific menus and described in the [[SEED_Viewer_Manual/Menu|Menu Overview]].

The general information about an organism include name, taxonomy id (linked to NCBI), the domain (Bacteria, Archeae or Eukaryota) as well as some information about the genome (contigs, subsystems, genes). The icon next to the taxonomy id leads to a Wikipedia page for that organism (the icon only shows up if there exists a Wikipedia page).

If you click on '''click for full list''', you will find more specific information about the organism.

[[Image:OrgsMenuGeneral.png]]

=== Browse, Compare and Download ===

The little [[WebComponents/Tabview|TabView]] next to the general information offers links to browse, compare and download the organism. These function are also available using the Organism menu.

'''Browse'''

Clicking the '''here''' link will lead to the [[SEED_Viewer_Manual/GenomeBrowser|Genome Browser]] for the selected organism.
It lets you browse the features of your organism.

[[Image:OrgsBrowse.png]]

'''Compare'''

Different kinds of comparisons of your selected organism to other organisms are available here (the function-based [[SEED_Viewer_Manual/CompareMetabolicReconstruction|Compare Metabolic Reconstruction]] will enable you to see the metabolic reconstruction of your selected organism against that of another one. The sequence-based [[SEED_Viewer_Manual/MultiGenomeCompare|Multi Genome Compare]] shows a table and a graphics comparing a selected set of organisms projected against your chosen one (BLAST-based). To project the metabolic capabilities of your organism on KEGG maps, use link to the [[SEED_Viewer_Manual/KEGG|KEGG]] page. Blasting against your organism is enabled using the [[SEED_Viewer_Manual/BLASTOrganism|BLAST]] link.

[[Image:OrgsCompare.png]]

'''Download'''

This tap provides a link to the [[SEED_Viewer_Manual/DownloadOrganism|Download Organism]] page.

[[Image:OrgsDownload.png]]

=== Subsystem Information ===

This part of the Organism Page deals with the subsystems present in your organism. The information is organized in a tab view, where the first tab shows a graphical overview of the subsystem information, while the second part lists all features in subsystems in a [[WebComponents/Table|Table]].

'''(1) Subsystem Statistics'''

The leftmost bar chart (Subsystem Coverage) depicts the percentage of features from the selected organism that are in subsystems.

In the middle the pie chart shows the distribution of subsystem categories in the organism. Hovering over the slices will inform you about the category you're looking at and the number of genes that fall in that category.

Right to the pie chart, you can find the Subsystem Feature Counts. The slices in the pie chart are presented in a tree view. Clicking the '''+''' signs will open a category and show the subcategory. Clicking the '''+''' of a subcategory will show the subsystems in that subcategory that are present in the organism. The links of the subsystems will open a [[SEED_Viewer_Manual/Subsystems|Subsystems Page]] for that subsystem. Behind all (sub)categories and subsystem you can find the number of genes that are present in the subsystem for that organism.

[[Image:OrgsSubsystems.png]]

'''(2) Features in Subsystems'''

Click on the second tab of the tab view to get the tabular view of the Features in Subsystems.
The [[WebComponents/Table|Table]] shows all the Subsystem Category, Subcategory, Subsystem Name, the Functional Role and the Feature Name of all features in subsystems in the organism.

The Subsystem links again lead to the [[SEED_Viewer_Manual/Subsystems|Subsystems]] page. Functional Role links will show the [[SEED_Viewer_Manual/FunctionalRoles|Functional Role]] page for that role. Feature links go to the [[SEED_Viewer_Manual/Annotation|Annotation page]] for that feature.

[[Image:OrgsFeatures.png]]

SEED Viewer Manual

2008-10-31T13:38:49Z

TobiasPaczian:

The SEED is a framework to support comparative analysis and annotation of genomes. The SEED Viewer allows you to explore the curated genomes that have been produced by a cooperative effort that includes Fellowship for Interpretation of Genomes (FIG), Argonne National Laboratory, the University of Chicago and teams from a number of other institutions.

These pages will cover the usage of the different pages within the Seed Viewer.

=== Home ===

=== Subsystem Select ===

=== Subsystems ===

=== Functional Role ===

=== FigFams ===

=== Annotation ===

=== Evidence ===

=== Blast ===

=== Sequence ===

=== Browse Genome ===

=== Organism Select ===

=== Organism Overview ===

=== Kegg ===

Backend Documentation

2007-10-05T20:09:35Z

TobiasPaczian:

The SeedViewer, RAST-Server and MG-RAST-Server were developed in an Web Application Framework developed by Daniel Paarmann and Tobias Paczian. Here you will find the links to tutorials and documentation.

* [[Web Application]]
* [[Web Components]]
* [[Persistent Perl Objects]]

Persistent Perl Objects

2007-10-05T20:09:22Z

TobiasPaczian:

The Persistent Perl Objects (PPO) provide a functionality to store perl objects persistently in a mySQL database.

== Overview ==

The PPO allows you to create an object schema in XML, which will be used to generate:

* an SQL file to create the underlying database
* a set of perl modules to create, read, update and delete objects
* a set of perl stub modules to create custom access methods for the objects if desired

On this page you will get a short introduction on how to use the PPO. A more detailed example can be found at [[PPO Example]].
You can find the definition of the XML at [[PPO XML Definition]].

== Source ==

The PPO module is checked into CVS. If you wish to use it, check it out to your cvs working directory and make sure it is in your path so the perl interpreter can find it. Something like the following should happen:

username@biologin-1:~/cvs$ cvs co PPO
Enter passphrase for key '/home/username/.ssh/id_rsa':
cvs checkout: Updating PPO
U PPO/.cvsignore
U PPO/DBMaster.pm
U PPO/DBObject.pm
U PPO/DBObjectCache.pm
U PPO/DBSQLArray.pm
U PPO/Makefile
U PPO/PPOBackend.pm
U PPO/PPOGenerator.pm
U PPO/generate.pl
cvs checkout: Updating PPO/PPOBackend
U PPO/PPOBackend/MySQL.pm
U PPO/PPOBackend/SQLite.pm

== Usage ==

First, create a directory to store your project files. Within this directory, create an XML file to describe your object schema. The XML must have the following format:

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="ProjectName1">
<object label="ObjectName1">
<scalar label="attributeName1" type="int" mandatory="1" />
<scalar label="attributeName2" type="CHAR(25)" />
<scalar label="attributeName3" type="text" default="-" />
<object_ref label="attributeName6" type="ProjectName1::ObjectName7" />
<array>
<object_ref label="attributeName4" type="ProjectName2::ObjectName2" />
</array>
<array>
<scalar label="attributeName5" type="boolean" />
</array>
<unique_index>
<attribute label="attributeName1" />
<attribute label="attributeName2" />
</unique_index>
</object>
</project_space>

After creating the schema file, you can call the generate script from the PPO to
# create the perl modules and
# create the PPO database on your database system.

generate.pl -xml xml_file -perl_target target_dir/

This will create a perl modules for your schema and a subdirectory with the neccessary ObjectBase.pm file which contains the access methods for your objects. Within this directory, you will also find a separate perl module for every object type in your schema. These files are stubs that allow you to customize the access methods to the according objects.

Note: the trailing '/' is important for the -perl_target parameter!

generate.pl -xml xml_file -backend db_backend -database db_name
e.g.: generate.pl -xml xml_file -backend MySQL -database my_db_name -user root

Run this command to create database on your database host. For this to work best, you have to be on the machine the database server runs on (in our case that's biofiler).

The setup of your schema is now complete. The following example will demonstrate how to use it in your code.

# include the Database Master Module
use DBMaster;

# initialize a DBMaster object
my $dbmaster = DBMaster->new(-database => 'my_db_name');

# create an object, passing attributes as a hash
my $new_object = $dbmaster->MyObject->create( { attribute1 => 'value1',
attribute2 => 'value2' } );

# it's a good idea to check what you got back
unless (ref $new_object) {
# substitute with a more appropriate reaction
die "Unable to create object.";
}

# change an attribute value
$new_object->attribute1( 'new_value' );

# retrieve an attribute value
my $value = $new_object->attribute1();

# get a single object, using an indexed attribute
my $new_object2 = $dbmaster->MyObject->init( { key_attribute1 => 'value1' } );

# get all objects that match the passed attribute values
my $object_list_array_reference = $dbmaster->MyObject->get_objects( { attribute1 => 'value1' } );

foreach (@$object_list_array_reference) {
# do something with each element of that array
}

# delete an object (and remove it from the database)
$new_object->delete();

PPO XML Definition

2007-10-05T20:07:18Z

TobiasPaczian:

On this page you will find the definition of the XML used to generate a PPO object schema. To clarify the descriptions below note the following. The '''XML schema''' is the representation of an '''Object schema'''. The term '''attribute''' may be used in both contexts, but refers to different things.

== Document ==

A document must start with the following tag:

<?xml version="1.0" encoding="UTF-8"?>

'''Note:''' All chosen names within an XML-definition '''may not''' be from a list of reserved words (across all supported database backends). A good starting point what to avoid is the list of [http://dev.mysql.com/doc/refman/5.1/en/reserved-words.html MySQL reserved words].

== XML Tags ==

=== project ===

Each project is encapsulated within a single database. Multiple projects may be hosted on one database-server. Projects that are to interact with each other '''must''' be hosted on the same database-server. The project tag surrounds the description of all objects within this project. The name of the project is reflected in the '''label''' attribute of the project tag. This will also be the name of the directory the generated perl-modules will reside. Projects may contain object elements.

<project label="MyProjectName">
...
</project>

=== object ===

Objects must reside inside of projects. They represent the types of data-objects which can be stored, retrieved and manipulated using the PPO. The object tag must be closed. The object must be named using the '''label''' attribute. This is the name the object can be accessed through. Objects may contain elements, representing their object-attributes and indices.

<object label="MyObjectName">
...
</object>

=== scalar ===

The scalar element represents an attribute of an object and may only appear within an object element. The label attribute of this element will be the name of the object attribute. The type attribute can be any of the following
data types (the exact size and implementation of each data type depends on the backend):
* BOOLEAN: true or false
* INTEGER: signed integer value
* FLOAT: signed floating-point number
* TIMESTAMP: timestamp as number of seconds since the epoch
* CHAR(n): field of n characters
* TEXT: text field (eg. 64kb)
* TEXT LONG: large text field (eg. 4GB)
* BLOB: data blob, stored as input
* BLOB LONG: large data blob

<scalar label="myAttributeName" type="INTEGER" />

=== object_ref ===

The object_ref element represents a reference to an object which is an attribute of the surrounding object. The label attribute of this element will be the name of the object attribute. The type attribute can be any object name; it may refer to objects within the same project or to object in other projects. If the referenced object is not stored in the same database, the type attribute must be preceeded by ''' 'MyProjectName::' '''.

<object_ref label="myObjectAttributeName" type="ObjectTypeWithinThisProject" />

or

<object_ref label="myObjectAttributeName" type="MyProjectName::ObjectTypeWithinOtherProject" />

=== array ===

The array element represents an attribute of the surrounding object which is an array. Arrays must consist exactly one instance of either a scalar or an object_ref.

<array>
<scalar label="myObjectAttributeName" type="INTEGER" />
</array>

or

<array>
<object_ref label="myObjectAttributeName" type="MyObjectType" />
</array>

=== index ===

The index element defines a mySQL index for this object for faster accession. Any combination of the scalar attributes of an object may be indexed, however, you may not index on arrays or object references. Each attribute to be part of the index must be listed via an attribute element. The attribute elements label attribute must be the name of the object attribute to be part of the index. You may create any number of indices.

<index>
<attribute label="myObjectAttributeNameA">
<attribute label="myObjectAttributeNameB">
...
</index>

=== unique_index ===

The unique_index element defines a set of attributes for an object which in combination must be unique. Any combination of the scalar attributes of an object may be indexed, however, you may not index on arrays or object references. Each attribute to be part of the index must be listed via an attribute element. The attribute elements label attribute must be the name of the object attribute to be part of the index. You may create any number of indices.

<unique_index>
<attribute label="myObjectAttributeNameA">
<attribute label="myObjectAttributeNameB">
...
</unique_index>

Creating a unique index will cause an '''init''' method to be created for this combination of attributes, allowing you access to instances of this object.

my $object = $dbmaster->myObject->init( { attribute1 => 'value1',
attribute2 => 'value2' } );

PPO Example

2007-10-05T20:06:57Z

TobiasPaczian:

== Introduction ==

The PPO allows you to use the object orientation of perl, with persistent store of the object in mySQL. The objects you create with the PPO are a direct representation of the database, meaning that changes to an object will immediately be stored. On this page, you will get a detailed example of the usage of the PPO. For a short overview, please refer to [[Persistent Perl Objects]].

This guide is split into six parts:

* setup of PPO
* creation of an object schema
* generation of the modules
* using PPO in your scripts
* customize access to objects
* troubleshooting

== Setup ==

For the course of this example, let us assume we want to create a little application that handles the management of users. We will call this application UserManagement. The programmer doing this will be called Joe User, his login is juser.

Since we are experimenting with new stuff, we want to do this in our sandbox. If your environment does not automatically do this, you must first source the config file, depending on your shell, either config.sh or config.csh.

cd ~/FIGdisk/config/
source fig-user-env.sh

or

cd ~/FIGdisk/config/
source fig-user-env.csh

The source code of PPO resides in CVS, so we now switch to the main source directory and check out PPO. Note that you only need the -d option, if you have not automatically done so in your environment. You must put your login in the string where it says juser.

cd ~/FIGdisk/dist/releases/current/
cvs -d :ext:juser@biocvs.mcs.anl.gov:/disks/cvs/bio checkout PPO

Something like the following should happen:

cvs checkout: Updating PPO
U PPO/.cvsignore
U PPO/DBMaster.pm
U PPO/DBObject.pm
U PPO/DBObjectCache.pm
U PPO/DBSQLArray.pm
U PPO/Makefile
U PPO/PPOBackend.pm
U PPO/PPOGenerator.pm
U PPO/generate.pl
cvs checkout: Updating PPO/PPOBackend
U PPO/PPOBackend/MySQL.pm
U PPO/PPOBackend/SQLite.pm

The PPOGenerator.pm contains the functionality to create the neccesary files from the object schema you create, so you can access your objects. The generate.pl script is called to generate the perl modules and setup the databases. The DBMaster.pm, DBObject.pm, DBSQLArray.pm and DBObjectCache.pm contain the core functionality of PPO. The PPOBackend.pm module and it's subdirectory provide the PPO with access to different database technologies (currently MySQL and SQLite).

== Object Schema ==

Before we can create an object schema for our little application, we create a directory for it.

mkdir ~/FIGdisk/dist/releases/current/UserManagement

Within this directory we create the schema file with the text editor of your choice. In our example, the file will be called '''UserManagement.xml'''.
To start off, we tell the xml, that we are using xml.

<?xml version="1.0" encoding="UTF-8"?>

Then we make an opening and closing tag for our project. PPO supports the integration of multiple schemata into one superspace. Our user management for example, might be part of a larger application. Other schemata might be referencing to objects in our UserManagement space. This larger scale concept is called '''Superspace'''. Since we have no large scale concept yet, we leave the superspace blank.

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="UserManagement" superspace="">

</project_space>

Now we are ready to create the first object. Every object needs a name and since we want to create a user management, we need a User. The user object should also have some attributes, e.g. firstName, lastName, login and password. Each user must have a login, so we make that attribute mandatory to make sure a user object cannot be created without a login.

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="UserManagement" superspace="">

<object label="User">
<scalar label="firstName" type="CHAR(250)" />
<scalar label="lastName" type="CHAR(250)" />
<scalar label="login" type="CHAR(250)" mandatory="1" />
<scalar label="password" type="CHAR(250)" />
</object>

</project_space>

Every attribute must have a type. In case of scalar attributes, this can be any valid mySQL data type. You can find information about mySQL data types [http://dev.mysql.com/doc/refman/5.1/en/data-types.html here].

When choosing names for Objects and their attributes, bear in mind that you may not use words reserved by mySQL. A current list of these words can be found [http://dev.mysql.com/doc/refman/5.1/en/reserved-words.html here].

Now we also want to make sure no two users get the same login. To achieve this we need to create an index. To create an index, include all attributes that should be contained in the index. If we assume for example that every user is unique if you take a combination of first and last name, include both firstName and lastName inside the index tag. Since there might to two people with the same first and last name, we rather use the login as the index. This will make sure no two users will get the same login. Also we want to introduce a default value. We will default the password for every user to 'secret'. Of course you know that in a real application you would a) encrypt the password and b) never set a default password.

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="UserManagement" superspace="">

<object label="User">
<scalar label="firstName" type="CHAR(250)" />
<scalar label="lastName" type="CHAR(250)" />
<scalar label="login" type="CHAR(250)" mandatory="1" />
<scalar label="password" type="CHAR(250)" default="secret" />
<index>
<attribute label="login" />
</index>
</object>

</project_space>

Multiple indices require multiple index tags. However, it is unlikely you will need more than one index for one object type.

To make things a little more complex, we would like to store the organization of every user. Since multiple users are likely to share the same organization, we want to create a new object type Organization to maintain normalization. The User object will then receive an attribute which is a reference to an Organization object. In this case, the type of the attribute is the name of the referenced object type. To make sure no two organizations have the same name, we index the name of the organization. This will also allow us to init an Organization object via its name.

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="UserManagement" superspace="">

<object label="User">
<scalar label="firstName" type="CHAR(250)" />
<scalar label="lastName" type="CHAR(250)" />
<scalar label="login" type="CHAR(250)" mandatory="1" />
<scalar label="password" type="CHAR(250)" />
<index>
<attribute label="login" />
</index>
<object label="organisation" type="Organisation" />
</object>

<object label="Organisation">
<scalar label="name" type="CHAR(255)" mandatory="1" />
<scalar label="abbreviation" type="CHAR(255)" />
<scalar label="url" type="CHAR(255)" />
<index>
<attribute label="name" />
</index>
</object>

</project_space>

The last thing we do is to introduce an array attribute. We want every user to have a list of rights, so we can differentiate which user may do what in our little application.

<?xml version="1.0" encoding="UTF-8"?>
<project_space label="UserManagement" superspace="">

<object label="User">
<scalar label="firstName" type="CHAR(250)" />
<scalar label="lastName" type="CHAR(250)" />
<scalar label="login" type="CHAR(250)" mandatory="1" />
<scalar label="password" type="CHAR(250)" />
<index>
<attribute label="login" />
</index>
<object label="organisation" type="Organisation" />
<array>
<scalar label="rights" type="CHAR(255)" />
</array>
</object>

<object label="Organisation">
<scalar label="name" type="CHAR(255)" mandatory="1" />
<scalar label="abbreviation" type="CHAR(255)" />
<scalar label="url" type="CHAR(255)" />
<index>
<attribute label="name" />
</index>
</object>

If you want to have multiple array attributes within one object, put them all in the same array tag. You may also have array attributes which are references to objects. Be careful though, usually object array attributes can be easily substituted by refining the schema and they are computationally very expensive.

== Module Generation ==

Now that the object schema is complete, we can generate the modules with the generate script. The script is located in the PPO directory and must be called with a set of parameters.

perl ~/FIGdisk/dist/releases/current/PPO/generate -f schemafilename -t targetdirectory -d databasename

In our case the schemafilename will be '''UserManagement.xml''', the target directory will be '''~/FIGdisk/dist/releases/current/UserManagement/''' and the database name will be '''UserManagement'''. This will produce the following files:

UserManagement.pm
UserManagement.sql
UserManagement/ObjectBase.pm
UserManagement/User.pm
UserManagement/Organization.pm

Now you can setup the mySQL database by just calling

mysql -u root < UserManagement.sql

This will generate all necessary tables for you. You are now ready to use the object schema you created. However, the modules User.pm and Organization.pm allow you to customize all calls to your objects. You can read more about this in the '''Customize''' section.

== Example Script ==

Now we will create a little script called user_management.pl which will use our freshly created object schema. To be nice we use strict and warnings and for the PPO we need to use DBMaster. Then the first thing we do is get a DBMaster object. This is our general access mechanism to all features of PPO. The only argument the DBMaster needs is the database name.

use strict;
use warnings;
use DBMaster;

my $dbmaster = DBMaster->new('UserManagement');

Using the DBMaster object, we can now create a new User object. We pass all attributes to the creator using a hash structure. We can omit any attributes we wish, except for the madatory attribute login. Also, we created and index on login, so we may not create objects with a value for login already posessed by another object. To ensure this does not happen, we try to init a User object with the login we create.

my $login = 'juser';
my $firstName = 'Joe';
my $lastName = 'User';
my $password = 'secret';

my $user;
unless ( $user = $dbmaster->User->init( { login => $login } ) ) {
$user = $dbmaster->User->create( { firstName => $firstName,
lastName => $lastName,
login => $login,
password => $password } );
}

Now the new_user variable will contain a reference to the newly created object. If the object creation failed, the variable will be undef. Now let's create another object, this time of the type Organization.

my $org_name = 'Acme Industries';
my $org_abbrev = 'AI';
my $org_url = 'www.acme.com';

unless ( $dbmaster->Organization->init( { name => $org_name } ) ) {
my $new_organization = $dbmaster->Organization->create( { name => $org_name,
abbreviation => $org_abbrev,
url => $org_url } );
}

Joe User is part of Acme Industries, so let us add this information to his user object.

$new_user->organization( $new_organization );

That was easy. Now let's examine if it all worked correctly and print the information in the user object.

print "User Summary\n";
print "First Name : " . $new_user->firstName() . "\n";
print "Last Name : " . $new_user->lastName() . "\n";
print "Login : " . $new_user->login() . "\n";
print "Password : " . $new_user->password() . "\n";
print "Organization : " . $new_user->organization->name() . "\n";

That will print out the data stored in our newly created objects. Let us imagine we have created a number of users and we want to get them all.

my $all_users = $dbmaster->User->get_objects( {} );
foreach my $user (@$all_users) {
print $user->firstName . " " . $user->lastName . "\n";
}

Now imagine that Acme Industries went bankrupt and all their users should be deleted from our database.

my $acme = $dbmaster->Organization->init( { name => 'Acme Industries' } );
my $acme_users = $dbmaster->User->get_objects( { organization => $acme } );
foreach my $acme_user ( @$acme_users ) {
$acme_user->delete();
}

This concludes the PPO example. The next chapter talks about customization of your object modules.

== Customize ==

The PPO allows you to customize the access methods for your objects, you can even create new methods. Let's pick up the example from above about the UserManagement. Imagine you always want to retrieve the list of users, ordered by name. The normal retrieval method '''get_objects''' would retrieve the data in the order of creation by default. The following example shows how this could be handled by overwriting the get_objects method.

UserManagement/User.pm

package WebApplicationServer::User;

use strict;
use warnings;

1;

# this class is a stub, this file will not be automatically regenerated
# all work in this module will be saved

sub get_objects {
# get the parameters given to the function
my ($self, $values) = @_;

# call the original method
my $objects = $self->SUPER::get_objects($values);

# do the sorting
my @sorted_objects = sort { $a->lastName cmp $b->lastName || $a->firstName cmp $b->firstName } @$objects;

# return the result
return \@sorted_objects;
}

== Troubleshooting ==

'''Problem:''' I call generate.pl and it tells me 'cannot open mysql_reserved'.

'''Solution:''' You must call generate.pl from the PPO directory, since mysql_reserved is expected to be in the directory you call generate.pl from.

Web Components

2007-10-05T20:05:37Z

TobiasPaczian:

Web Components are self contained objects that produce html output for standard application components that can be used in the context of a [[Web Application]].

== Overview ==

Here you will find a comprehensive list of the currently available Web Components and their parameters. To include a Web Component in your application, follow the instructions on the [[Web Application]] page.

== Component List ==

=== Table ===

In its simplest form, this merely displays a table. The component also offers the functionality for column sorting, column filtering, browsing, highlighting, onclick-events for cells, popup menus for cells and an export function.

'''Example'''

[[Image:Example_table.png]]

This table was created using the following code

$self->application->register_component('Table', 'testtable');

my $table_component = $self->application->component('testtable');
$table_component->data([ ['A','B','C'], ['D','E','F'], ['G','H','I'] ]);
$table_component->columns( [ { 'name' => 'Col A', 'filter' => 1 },
{ 'name' => 'Col B' },
{ 'name' => 'Col C', 'filter' => 1, 'operators' => [ 'like', 'unlike' ] } ] );
$table_component->show_top_browse(1);
$table_component->show_bottom_browse(1);
$table_component->items_per_page(2);
$table_component->show_select_items_per_page(1);
print $table_component->output();

'''Parameters'''

* '''data''' (arrayref of arrayrefs of strings)
The table data must be a list of rows, each of which is a list of cells. For each cell you have two options.
:* ''pass a string'' - this string will then become the content of the cell
:* ''pass a hash'' - the hash allows you to pass additional options:
::* '''data''' - the data of the cell
::* '''highlight''' - an integer defining the highlight color of the cell:
:::The integers represent different highlighting colors
:::* 0: no highlighting
:::* 1: green
:::* 2: blue
:::* 3: red
:::* 4: yellow
::* '''menu''' - a menu as used in the Hover component described below. This must be a hash with the keys 'titles' and 'links', each pointing to array references with the according entries for the titles and the links of the menu
::* '''tooltip''' - html to be displayed in the tooltip of this cell.
::* '''onclick''' - the url the onclick event of the cell should take the page to

* '''columns''' (arrayref of (hashrefs or strings))
: If you do not pass hashrefs, the strings will be used as the column header
:* ''name:'' the text in the column header
:* ''sortable:'' a boolean indicating whether clicking the column header will sort this column. The sort function will determine the kind of data given the first cell of the column. Recognized data types are:
::* ''date'': /^\d\d[\/-]\d\d[\/-]\d\d\d\d$/ or /^\d\d[\/-]\d\d[\/-]\d\d$/
::* ''numerical'': /^\d+\.{0,1}\d*$/
::* ''e-value'': /^\d+\.{1}\d+e[+-]{1}\d+$/
::* ''alphabetical'': everything unrecognized by the above
:* ''filter:'' a boolean indicating whether this column should have a filter box
:* ''operator:'' the operator the filter will use by default. May be either one of: '''like''', '''unlike''', '''equal''', '''unequal''', '''less''', '''more'''. You can also set the operator to '''combobox''' which will create a combobox as a filter, filled with every distinct value of that column.
:* ''operators:'' the selection of operators the user may choose from when filtering. This must be an array of the above.
Each element in the columns array represents one column. These elements may have several properties, only '''name'' being mandatory.
:* ''width:'' the width of the column in pixels.
:* ''visible:'' a boolean indicating whether this column is to be displayed. Invisible columns will be added to the control panel.
:* ''show_control:'' a boolean indicating whether to display this column in a control panel above the table. The column headers of those columns will appear in the control panel, allowing to sort/filter the columns, without the need of displaying them.

'''Options'''

* '''items_per_page''' (int)
Determines the number of rows that will be displayed at a time. If you specify this, you should choose at least one of the browse options, so the user can browse through the data.

* '''show_export_button''' (boolean or hash)
If this is a boolean, then a value of true will display a button to export the table above the table.
If this is a hash, you have multiple options for the export button:
:* '''title''': the title of the button
:* '''strip_html''': The export will strip any html tags from cells before exporting
:* '''unfiltered''': Instead of the normal behavior, where only the cells that passed the current filter will be exported, all cells are exported
:* '''hide_invisible_columns''': All cells in columns currently marked as invisible will not be exported

* '''show_select_items_per_page''' (boolean)
If true will allow the user to select how many rows should be displayed at a time.

* '''show_top_browse''' (boolean)
If true will display browsing functions above the table.

* '''show_bottom_browse''' (boolean)
If true will display browsing functions below the table.

* '''offset''' (int)
The number of rows that will initially not be show from the beginning of the dataset.

* '''width''' (int)
The width of the table in pixels.

'''Additional Functions'''

The table module supports a set of javascript functions for manipulation.

* '''show_column''' (table_id, colum_index)
This will make a column in the table visible.

* '''hide_column''' (table_id, column_index)
This will render a column invisible.

''Coding Example''

Assuming you have a table component that is already filled with data, you could create buttons that would show hide a certain column like this:

my $table = $self->application->component('myTable');
print "<input type='button' value='Hide Column 2' onclick='hide_column(\"" . $table->id() . "\", \"2\");'>";
print "<input type='button' value='Show Column 2' onclick='show_column(\"" . $table->id() . "\", \"2\");'>";

'''Note:''' The id you need to pass to the javascript function is not what you ''call'' your component with (the parameter you pass to $app->component), but rather the ''id'' ($myComponent->id() ).

=== TabView ===

Creates a tabular view.

'''Example'''

[[Image:Example_TabView.png]]

This Tabular View was created with the following code

$self->application->register_component('TabView', 'TestTabView');

my $tab_view_component = $self->application->component('TestTabView');
$tab_view_component->width(600);
$tab_view_component->height(180);
$tab_view_component->add_tab('Tabulator A', 'This is the content of tab a');
$tab_view_component->add_tab('Tabulator B', 'This is the content of tab b');
$tab_view_component->add_tab('Tabulator C', 'This is the content of tab c');
$tab_view_component->add_tab('Tabulator D', 'This is the content of tab d');
print $tab_view_component->output();

'''Parameters'''

* '''add_tab''' (string, string)
The first string passed will become the title of the tab, the second string will become the content od the tab.

'''Options'''

* '''width''' (int)
The width of the component in pixels.

* '''height''' (int)
The height of the component in pixels. '''Note:''' The height of the tab header will be added to this number.

* '''default''' (int)
The tab initially in front.

=== FilterSelect ===

Creates a select box whose content is filtered by infix search with the string typed into an input field. The current best match will be selected.

'''Example'''

[[Image:Example_FilterSelect.png]]

This filter select was created using the following code

$self->application->register_component('FilterSelect', 'TestFilterSelect');

my $filter_select_component = $self->application->component('TestFilterSelect');
$filter_select_component->labels( [ 'Monkey', 'Donkey', 'Sponkey', 'Tronkey', 'Plonkey', 'Veronkey' ] );
$filter_select_component->values( [ 'A', 'B', 'C', 'D', 'E', 'F' ] );
$filter_select_component->size(8);
$filter_select_component->width(250);
$filter_select_component->name('TestFilter');
print $filter_select_component->output();

'''Parameters'''

* '''labels''' (array of strings)
These will become the labels of the selectable items.

* '''values''' (array of strings)
These will become the values of the selectable items.

* '''name''' (string)
The name of the select component.

'''Options'''

* '''size''' (int)
The number of items appearing at a time.

* '''width''' (int)
The width of the component in pixels.

=== Login ===

Creates a login form.

'''Example'''

[[Image:Example_Login.png]]

The login was created using the following code

$self->application->register_component('Login', 'TestLogin');

my $login_component = $application->component('Login');
$login_component->small_login(1);
print $login_component->output();

'''Parameters'''

''none''

'''Options'''

* '''small_login''' (boolean)
Setting this to true will return a smaller version of the login component.

=== Register ===

Creates a form to register a user to an application.

'''Example'''

[[Image:Example_Register.png]]

This register component was created using the following code

$self->application->register_component('Register', 'TestRegister');

my $register_component = $self->application->component('TestRegister');
print $register_component->output();

'''Parameters'''

''none''

'''Options'''

''none''

=== GenomeDrawer ===

Draws genome related graphics.

'''Example'''

[[Image:ExampleGenomeDrawer.png]]

This example was produced using the following code:

$self->application->register_component('GenomeDrawer', 'GD1');
my $gd = $application->component('GD1');
my $line_data = [ { 'start' => 0, 'end' => 100, 'type' => 'arrow', 'title' => 'A', 'color' => 2, 'zlayer' => 1,
'description' => [ { 'title' => 'title a', 'value' => 'value a' } ] },
{ 'start' => 55, 'end' => 70, 'type' => 'smallbox', 'title' => 'subA', 'color' => 1, 'zlayer' => 2 },
{ 'start' => 210, 'end' => 110, 'type' => 'arrow', 'title' => 'B', 'color' => 3, 'zlayer' => 2 },
{ 'start' => 250, 'end' => 390, 'type' => 'smallbox', 'title' => 'C', 'color' => 4, 'zlayer' => 2 },
{ 'start' => 450, 'end' => 600, 'type' => 'bigbox', 'title' => 'D', 'color' => 5, 'zlayer' => 2 },
{ 'start' => 650, 'end' => 800, 'type' => 'box', 'title' => 'E', 'color' => 6, 'zlayer' => 2 },
{ 'start' => 900, 'end' => 1190, 'type' => 'ellipse', 'title' => 'F', 'color' => 7, 'zlayer' => 2 } ];
my $line_config = { 'title' => 'Line 1 which has a really long title',
'short_title' => 'Line 1',
'title_link' => 'http://www.google.de',
'basepair_offset' => 0 };
$gd->width(600);
$gd->show_legend(1);
$gd->window_size(1200);
$gd->line_height(30);
$gd->display_titles(1);
$gd->add_line($line_data, $line_config);
print $gd->output;

'''Parameters'''

* '''add_line''' (line_data, line_config)
The line_data structure is an array reference of hashreferences, each hash representing one item of the line. The items have the following attributes, some of which are optional:

: '''Mandatory'''
:* ''start''
:: The starting base of the item
:* ''end''
:: The end base of the item
: '''Optional'''
:* ''title''
:: The title of the item, appearing in it's popup box or above the item, if the item is an arrow and the '''display_titles''' option is set.
:* ''type''
:: The shape of the item. You can see examples of each shape in the graphic above.
:: Currently valid types are:
::* box
::* bigbox
::* smallbox
::* smallbox_noborder
::* ellipse
::* arrow
:* ''zlayer''
:: The position of the item on the z-axis. Higher zlayers will appear over lower zlayers.
:* ''color''
::This can be either a scalar from 1 to 20, choosing the according color from the current color theme, or an array reference with three integers specifying RGB values.
:* ''description''
:: This will produce a popup box, appearing upon hovering over the item. Description is an array reference of hashes. The hashes have two entries:
::* title
::* value
:* ''links_list''
:: This will produce a context menu, appearing upon clicking the item. Links_list is an array reference of hashes. The hashes have two entries:
::* link
::* link_title
:* onclick
:: Any code passed to this will be executed upon the onclick event.

The line_config (optional) is a hashreference which represents the following attributes of a line:

:* ''title''
:: The title of the line (e.g. name of the organism) to be displayed in the legend. If the title is too long to fit the legend space, the short title will be displayed instead and the title will be displayed in a popup box upon hover over.
:* ''short_title''
:: The short title of the line to be displayed when the title is too long to fit into the designated legend space.
:* ''title_link''
:: The link to be executed when the title of a line is clicked.
:* ''basepair_offset''
:: the offset of basepairs the region. Default is 0.
:* ''no_middle_line''
:: This option will prevent a middle line from being drawn for this line.

'''Options'''

* '''width'''
: The width of the graphic part of the Genome drawer in pixels. Default is 800.
* '''show_legend'''
: Boolean indicating whether to show line descriptions on the left border. Default is false.
* '''legend_width'''
: Width of the legend part of the Genome drawer in pixels. Default is 100.
* '''display_titles'''
: Boolean indicating whether to display gene titles over the genes (arrows). Default is false.
* '''line_height'''
: The height of each line in pixels. Default is 30.
* '''window_size'''
: the number of basepairs in the displayed region. Default is 50.000.

=== Hover ===

Creates a set of hover menus and hover tooltips. These menus and tooltips can be added to any HTML element and may be triggered by any HTML event. The example code shows you how to attach a created menu or tooltip to your element.

'''Example'''

$self->application->register_component('Hover', 'TestHover');

my $hover_component = $application->component('TestHover');
$hover_component->add_tooltip( 'hover_test_1', 'Hello World' );
$hover_component->add_menu( 'hover_test_2', [ 'Yahoo', 'Google' ], [ 'http://www.yahoo.de', 'http://www.google.de' ] );
print $hover_component->output();
print "<img src='./Html/info.png' id='hover_test_1' onmouseover='hover(event, \"hover_test_1\");'>";
print "<img src='./Html/info.png' id='hover_test_2' onmouseover='hover(event, \"hover_test_2\");'>";

'''Parameters'''

''none''

'''Options'''

* '''add_tooltip''' (string, string, int, int)
Adds a new tooltip to the tooltip container. The first string passed must be the id of the html element the tooltip should refer to. The second string can be any type of HTML. This will become the content of the tooltip. The int arguments are width (in pixels) and timeout (in milliseconds) respectively, which are optional. Default width is 150px, default timeout 8000ms.

* '''add_menu''' (string, arrayref, arrayref, int, int)
Adds a new hover menu to the menu container. The first string passed must be the id of the html element the menu should refer to. The second and third argument must be references to arrays. The first array must contain the strings to be displayed as the titles of the menu entries. The second array must contain the urls the menu entries should link to. The int arguments are width (in pixels) and timeout (in milliseconds) respectively, which are optional. Default width is 150px, default timeout 10000ms.

=== Info ===

Creates an information container which can be collapsed. The expanded and collapsed version can be seen in the example. The collapse/expand occurs upon clicking on the 'i'.

'''Example'''

[[Image:Example_Info_1.png]] [[Image:Example_Info_2.png]]

This example was created using the following code:

$self->application->register_component('Info', 'TestInfo');

my $info_component = $application->component('TestInfo');
$info_component->content( '...Text here...' );
print $info_component->output();

'''Parameters'''

* '''content''' (string)
The content of the information container.

'''Options'''

* '''title''' (string)
The title of the information container.

* '''width''' (string)
The width of the information container as you would put as a css attribute (e.g. 200px or 15%).

* '''default''' (boolean)
If true the information container will be initially expanded, if false it will be collapsed.

=== HelpLink ===

Creates a little questionmark with a hover information. Clicking the symbol links to the wiki.

'''Example'''

[[Image:Example_HelpLink.png]]

This example was created using the following code:

$self->application->register_component('HelpLink', 'test_help_component');

my $help_component = $application->component('test_help_component');
$help_component->page('myWikiPage');
$help_component->title('myTitle');
$help_component->text('Short informative text.');
print $help_component->output();

'''Parameters'''

* '''text''' (string)
The content of the help hover.

* '''title''' (string)
The title of the help hover.

'''Options'''

* '''page''' (string)
The wiki page the help link will link to. Default is the value of title.

* '''wiki''' (string)
The base url of the wiki to link to. Default is 'http://www.theseed.org/wiki/'

* '''hover_width''' (int)
The width of the hover info box in pixels. Default is 150px.

=== PieChart ===

Creates a pie chart.

'''Example'''

[[Image:Example_PieChart.png]]

This example was created using the following code:

$self->application->register_component('PieChart', 'test_pie');

my $pie = $application->component('test_pie');
$pie->data( [ 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10, 10 ] );
print $pie->output();

'''Parameters'''

* '''data''' (array of int)
The array of values to be displayed.

'''Options'''

* '''size''' (int)
The size of the chart in pixels. Default is 400.

=== Ajax ===

Component for Ajax support. This will allow you to reload parts of your page, without having to reload the entire page. You can write any function in your WebPage module and call it via this mechanism. You will have access to the application object in that function. This means you have access to session information as well as any components which were registered in the original calling of your page.

'''Example'''

$self->application->register_component('Ajax', 'test_ajax');

print $application->component('test_ajax')->output();
print "<div id='ajax_target'></div>";
my $no_loading_image = 0;
print qq~<form id="ajax_source" action="javascript:execute_ajax('myFunction', 'ajax_target', 'ajax_source', 'loading_text', $no_loading_image);">~;
print "<input type='text' name='test_text' value='Hello World'><input type='submit'>";
print "</form>";

use URI::Escape;
my $text = uri_escape("Hello World");
print qq~<a href="javascript:execute_ajax('myFunction', 'ajax_target', 'test_text=~ . $text . qq~');">click me</a>~;

sub myFunction {
my ($self) = @_;
my $cgi = $self->application->cgi();
return $cgi->param('test_text');
}

'''Parameters'''

The actual parameters are passed to the '''execute_ajax''' javascript.

:* '''function'''
:: The name of the function in MyPage.pm which will return the content to be displayed in the target div.
:* '''target'''
:: The id of the div the result of the called function should appear in

'''Options'''

The options are passed to the '''execute_ajax''' javascript.

:* '''source'''
:: This can be either the id of a form whose content will be passed to the called function in MyPage.pm or a uri-encoded string of key-value pairs as shown in the example.
:* '''loading_text'''
:: This text will be displayed next to the loading image, displayed until the perl function returns the content. Default is: 'Loading...'.
:* '''no_loading_text'''
:: If set to 1, no loading text will be displayed. Default is 0.

=== Tree ===

Component to create treeviews of various kinds. Right now, only a very simple version is supported, but it is currently being expanded.

'''Example'''

[[Image:Example_Tree.png]]

This example was created using the following code:

$self->application->register_component('Tree', 'Testtree');

my $tree = $application->component('Testtree');
my $lvl1 = ['Grandfather A','Grandfather B','Grandfather C','Grandfather D'];
foreach my $l1 (@$lvl1) {
my $lvl2 = ['Father A','Father B'];
my $node = $tree->add_node( { 'label' => $l1 } );
foreach my $l2 (@$lvl2) {
my $lvl3 = ['Child A', 'Child B', 'Child C'];
my $child = $node->add_child( { 'label' => $l2 } );
foreach my $l3 (@$lvl3) {
$child->add_child( { 'label' => $l3 } );
}
}
}
print $tree->output();

'''Parameters'''

* '''add_node''' ( { 'label' => $label,
'expanded' => $expanded } )
Adds a node to the tree with the given label. The optional 'expanded' attribute is a boolean indicating whether the node is initially expanded or not. Default is false.

'''Options'''

* '''node->add_child''' ( { 'label' => $label,
'expanded' => $expanded } )
Adds a child to a node.

== Supporting Components ==

=== WebGD ===

The WebGD Component is used to produce Internet Explorer safe images. Since we want to support IE and IE does not support inline images, you should use WebGD anytime you create a component that creates inline images. WebGD functions in the same way that '''GD::Image''' does. It has one additional method '''image_src''' which returns you the src-part of the html image tag to display your image.

'''Usage'''
use WebGD;
my $image = WebGD::new($width, $height);
$image->line($x1, $y1, $x2, $y2, $color);
... draw your image ...
print "<img src='" . $image->image_src() . "'>";

This will detect whether the client is IE or another browser. IE will cause it to create a temporary file and link it, all other browsers support inline images, so WebGD will use base64 encoding to produce an inline image.

'''Caution'''

Make sure that the variables

''$temp_url''

and

''$temp''

are set correctly in you FIG_Config.pm, as those paths will be used by WebGD.

Web Application

2007-10-05T20:04:45Z

TobiasPaczian:

The Web Application is a framework to support fast, comprehesible and componentalized creation of applications on the web.

== Overview ==

The Web Application framework will take care of the structure of your application in the web. Main features include:

* menus
* user authentication
* page/action management
* WebComponents

The following tutorial will describe how to set up your own application in the web using the WebApplication framework.

== Setup ==

There are two modules required for the Web Application framework:

* WebApplication
* PPO

both must be checked out from the CVS. The following assumes you have set up a sandbox for your application. If you do not know how to set up a sandbox have bob do it ;) or go to [[Sandbox Setup]].

cd ~/public_html/my-app/dist/releases/current/
cvs co WebApplication
cvs co PPO

Now create a directory for your application.

mkdir MyApp
cd MyApp

Now we fill in the neccessary elements that customize your application. You need to create the following things:

* a '''cgi-script''' that becomes the centerpoint for your application
* a '''directory''' called '''WebPage''' that will contain your different pages
* an '''initial page''' for your application to display
* a '''template file''' that describes the layout of your pages (optional)
* a '''stylesheet''' that takes care of font-styles and the like (optional)
* a '''directory''' for the '''images''' you want on your pages (optional)

To get things going, perform the following steps:

cp ../WebApplication/example/example.cgi myApp.cgi
cp ../WebApplication/example/Example.Makefile Makefile
mkdir WebPage
cp ../WebApplication/example/Example.pm WebPage/MyFirstPage.pm
cp ../WebApplication/WebLayoutDefault.tmpl MyAppLayout.tmpl
mkdir images
cd images
cp ../../WebApplication/images/* .

As you can see, there are example files for all of these that you can modify.
At this point, your application is already up and running. Do a '''make''' and examine the result in the web:

http://bioseed.mcs.anl.gov/~juser/my-app/www/FIG/myApp.cgi

[[Image:MyFirstApp.png]]

The WebApplication comes with a default stylesheet (css) that defines colours and fonts and so on. It's likely that you want change those at some point. To do so:

go back to your working application directory: cd MyApp
mkdir css
cp ../WebApplication/css/default.css css/myapp.css

Now edit your myApp.cgi and replace the css filename in the following line:

$layout->add_css(TMPL_PATH.'/myapp.css');

== Your First Page ==

This is the demo page you have copied from the WepApplication directory. All it will do is print a page that reads 'Hello World'. When you go to the url of your application's script, this is the first page that will appear. This is because in the [[Web Application Script]] it is defined as the default first page.

package MyApp::WebPage::MyFirstPage;

use strict;
use warnings;

use base qw( WebPage );

1;

sub output {
my ($self) = @_;

my $content = "<h1>Hello World</h1>";

return $content;
}

The logic of the Web Application will perform the following checks to see which page should be displayed:

* was the cgi parameter '''page''' passed?
** '''Yes:''' check if the page '''$cgi->param('page')''' requires any rights to be displayed
*** if there are no rights required, display the page
*** if there are rights required and there is no user, display the login page. After the login page has been processed, recheck to display this page.
*** if there are rights required and the user does not possess them, display an error
*** if there are rights required and the user does possess them, display the page
** '''No:''' display the default first page
*** perform same authorization steps

=== Creating a new Page ===

If you wish to create a new page, simply create a new file in the '''WebPage''' directory of your application. You can copy the example file from the WebApplication directory as a template.

cd ~/public_html/myApp/dist/releases/current/myApp/WebPage/
cp ../WebApplication/Example.pm MyNewPage.pm

The name of the file, will be the value of the cgi page parameter which will display your page.

http://bioseed.mcs.anl.gov/~juser/myApp/www/FIG/myApp.cgi?page=MyNewPage

Would point to your new page.

=== Page Methods ===

When inside the your page module, you can access the inherited '''WebPage''' methods using

$self->method(params);

The following methods are available.

* '''title''' (string)
Sets the title information for this page. This will be displayed in the title bar of your browser.

* '''application'''
Returns the application object.

* '''name'''
Returns the name of the current page.

* '''url'''
Returns the url to the current page.

* '''start_form''' (string, hashref)
Returns an opening html form tag. The string passed will be the html id of the form ''(optional)''. The hash reference is used to preserve the current state. The keys will be inserted as '''hidden''' fields with their values set to the values of the according hash entry.

* '''end_form'''
Returns a closing html form tag.

The following are abstract functions which you can implement in your page.

* '''init'''
This should include all functionality which must be called ''prior'' to calling the '''output''' method of the page. Component registration using <br>
:'''$self->application->register_component('ComponentType', 'ComponentID');'''<br>
is an example of this.

* '''require_javascript'''
This must return an array reference. Each element in the array must be the filename of a java script file. This file will automatically be included in the header of the page. If this method is not implemented, no extra java script will be included for this page.

* '''require_css'''
This must return a string which must be the filename of the stylesheet file to be included for this page. If this method is not implementd, no extra stylesheet will be included for this page.

* '''required_rights'''
This must return an arrayref of arrayrefs. Each element in the array must be a rights tuple. These are explained in the [[Using Rights]] section. If this method is not implemented, no rights will be required to see this page.

=== Application Methods ===

Since every page you create inherits from '''WebPage''', you can access the application object using

my $application = $self->application;

The '''application object''' then offers the following functions

* '''session'''
This will return the '''session object'''. The session object then allows access to the following functions
:* '''user'''
:Returns the '''user object'''
:* '''get_entry'''
:Returns the name and parameters of the page last visited.

* '''cgi'''
Returns the '''cgi object'''

* '''error'''
Sets the applications error message. This will cause an error page to be displayed. No other content will be seen on the page. If you wish to display the normal content of the page and in addition some note to the user, you can use the '''add_message''' method.

* '''add_message'''
Adds a note or a warning to the page. This method takes two arguments, the first one can be either 'warning' or 'info', depending on which type of message you wish to add. The second parameter is the actual message.

* '''page'''
Returns the current page object.

* '''url'''
Returns the script url

* '''redirect'''
Causes the url passed to be loaded instead of the current one.

* '''register_component'''
Registers a component at the application. This component can be retrieved via the '''component' method.

* '''component'''
Retrieves a previously requested component object.

* '''register_action'''
Registers an action for this page with the application. If an unregistered action is called, an error will occur.

The following functions are usually only used in the [[Web Application Script]] of your application.

* '''default'''
Sets the default first page to load if no cgi page parameter is given.

* '''dbmaster'''
Sets the database master which will be used to crud user and session information.

* '''layout'''
Sets the WebLayout used to build the application pages.

==== Menus ====

* '''menu'''
Returns the '''menu object'''. The menu object then allows access to the following functions
:* '''add_category''' (category, url, target, right, sort_order)
:* '''delete_category''' (category)
:* '''get_categories'''
:* '''add_entry''' (category, entry, url, target)

=== Using Rights ===

The WebApplication also offers you the ability of '''Rights Management'''. This topic is described in detail at the [[WebApplication Rights]] page.

== [[Web Components]] ==

The ability to include standard components into your application is one of the main features of the Web Application framework. This will give you a short introduction on how to use these components. A comprehesive list with detailed feature descriptions of currently available components is available on the [[Web Components]] page.

There are two methods of the application object that refer to components.

$application->register_component('ComponentName', 'ComponentID');
my $component = $application->component('ComponentID');

The first one registers a component for your page. This means an actual instance of the component type you request is created and stored in the application. This instance can now be accessed by the second method by passing the ID you chose for this component instance. The registration of a component must be done in a pages '''init''' method. After retrieving the requested component from the application object, you can then access its methods. Typically, components have '''getter/setter''' functions to set their parameters and an '''output''' method to return html content you can print onto your page.

The following code is using the Login component as an example.

sub init {
my $self = shift;

$self->application->register_component('Login', 'MyLogin');
}

sub output {
my ($self) = @_;

my $content = "";

my $application = $self->application;
my $cgi = $application->cgi;

my $login_component = $application->component('MyLogin');
$login_component->small_login(1);
my $login = $login_component->output;

$content .= "<h1>Hello World</h1>" . $login;

return $content;
}

== Advanced Customizing ==

If you are merely designing an manipulating pages, there is no need for you to ever look at any files outside the '''WebPage''' directory of you application. If you are setting up the application however, you need to check the [[Web Application Template]] and the [[Web Application Script]]. There are also '''Stylesheets''' that you can modify and you probably wish to exchange some '''images''', like the logo.

Backend Documentation

2007-10-05T20:04:23Z

TobiasPaczian:

SEED Viewer Numbers

2007-08-15T17:48:08Z

TobiasPaczian: /* SeedViewer */

The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

=== MG-RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of sequences''
: This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.

* ''Total sequence length''
: This is the sum of the lengths of all submitted sequences.

* ''Average read length''
: This is the '''Total sequence length''' divided by the '''Number of sequences'''

* ''Longest sequence id'
: This is the identifier string of the longest sequence submitted.

* ''Longest sequence length''
: This is the length of the longest sequence submitted.

* ''Shortest sequence id''
: This is the identifier string of the shortest sequence submitted.

* ''Shortest sequence length''
: This is the length of the shortest sequence submitted

=== RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of features''
: This is the number of features the RAST-Server could identify in your uploaded genome and match to our database.

* ''Number of warnings''
: This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below.

* ''Number of fatal problems''
: This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish.

* ''Possibly missing genes''
:

* ''Convergent overlaps''
:

* ''Divergent overlaps''
:

* ''Same strand overlaps''
:

=== SeedViewer ===

On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome:

* ''Size''
: This is the number of basepairs of sequence of this genome.

* ''Number of Fragments''
: This is the number of fragments which included at least one coding sequence that could be matched to our database.

* ''Number of Subsystems''
: The number of different subsystem in which at least one member was found in the fragments of the genome.

* ''Number of Coding Sequences''
: The number of protein encoding genes found in the submitted fragments that matched against our database.

* ''Number of RNAs''
: The number of RNAs found in the submitted fragments that matched against our database.

* ''Protein Encoding Genes''
: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left.
: '''non-hypothetical'''
: This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein''
: '''hypothetical'''
: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)

* ''Subsystem Counts''
The numbers in the tree of the subsystem hierarchy represent the number of coding sequences which are part of the according group, subgroup, subsystem or role. Note that not every coding sequence is part of a subsystem and that a single CDS may be part of more than one subsytem.

SEED Viewer Numbers

2007-08-15T16:48:41Z

TobiasPaczian: /* SeedViewer */

SEED Viewer Numbers

2007-08-15T16:46:00Z

TobiasPaczian: /* SeedViewer */

The SeedViewer, RAST-Server and MG-RAST-Server offer you a large number of statistics and detailed numbers about your organism. The purpose of this page is to explain how we calculate these numbers and what they mean.

=== MG-RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of sequences''
: This is the total number of sequences submitted by the user for this genome. Not all of these will produce results later on. It is possible and very probable that some sequences can not be matched to anything in our database.

* ''Total sequence length''
: This is the sum of the lengths of all submitted sequences.

* ''Average read length''
: This is the '''Total sequence length''' divided by the '''Number of sequences'''

* ''Longest sequence id'
: This is the identifier string of the longest sequence submitted.

* ''Longest sequence length''
: This is the length of the longest sequence submitted.

* ''Shortest sequence id''
: This is the identifier string of the shortest sequence submitted.

* ''Shortest sequence length''
: This is the length of the shortest sequence submitted

=== RAST ===

On the details page of your organism, you will find the following numbers:

* ''Number of features''
: This is the number of features the RAST-Server could identify in your uploaded genome and match to our database.

* ''Number of warnings''
: This is the number of warnings issued by the pipeline while processing your genome. This refers to inconsistencies detected, which are not fatal to annotation, but which should be investigated further. The numbers for each type of warnings are listed below.

* ''Number of fatal problems''
: This is the number of problems which cause the pipeline to be unable to process your genome. These problems have to be addressed before the annotation process can finish.

* ''Possibly missing genes''
:

* ''Convergent overlaps''
:

* ''Divergent overlaps''
:

* ''Same strand overlaps''
:

=== SeedViewer ===

On the ''Organism Overview'' page, there are a number of statistical counts about the selected genome:

* ''Size''
: This is the number of basepairs of sequence of this genome.

* ''Number of Fragments''
: This is the number of fragments which included at least one coding sequence that could be matched to our database.

* ''Number of Subsystems''
:

* ''Number of Coding Sequences''
:

* ''Number of RNAs''
:

* ''Protein Encoding Genes''
: The numbers are given in absolute and percent value. They should add up to 100% (given rounding error) and their sum should be the equal to the number of coding sequences displayed on the left.
: '''non-hypothetical'''
: This is the number of coding sequences, which were annotated with a function which is not hypothetical. Values for hypothetical include a list of synonyms like ''hypothetical protein'' or ''putative protein''
: '''hypothetical'''
: This is the number of coding sequences which were assigned to be hypothetical (or a synonym)

SEED Viewer Numbers

2007-08-15T16:33:06Z

TobiasPaczian: /* MG-RAST */

SEED Viewer Numbers

2007-08-15T16:24:15Z

TobiasPaczian: /* Numbers in the SeedViewer, RAST Server and MG-RAST Server */